Fix cases that MiSeq samplesheet misses index or index2

[chuan-wang]

And some ruff linting.

[codecov]

Codecov Report

Attention: Patch coverage is 16.66667% with 10 lines in your changes are missing coverage. Please review.

Project coverage is 21.80%. Comparing base (6d7d339) to head (b5c8feb).

Files	Patch %	Lines
taca/illumina/Runs.py	0.00%	5 Missing ⚠️
taca/analysis/analysis.py	0.00%	3 Missing ⚠️
taca/illumina/Standard_Runs.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #420   +/-   ##
=======================================
  Coverage   21.79%   21.80%           
=======================================
  Files          28       28           
  Lines        3936     3944    +8     
=======================================
+ Hits          858      860    +2     
- Misses       3078     3084    +6     

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[sofiahag]

Wow, you're so fast, Chuan! ⚡

[chuan-wang]

Wow, you're so fast, Chuan! ⚡

Very tiny change :D

[sofiahag]

The code looks good to me!